|
| Status |
Public on Jun 15, 2019 |
| Title |
RNA-seq_iPSC-induced excitatory neurons_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-induced excitatory neurons
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-induced excitatory neurons
|
| Growth protocol |
Human primary fetal astrocytes were cultured according to the ScienCell protocol (catalog #1801).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (QIAGEN #74104) according to its protocol.
The TruSeq Stranded mRNA protocol from Illumina was followed for library construction (catalog #RS-122-2101).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LM007
|
| Data processing |
All reads were quality trimmed using TrimGalore 0.4.5 prior to further processing. For libraries having undergone paired-end sequencing, only the first read was used.
Reads were mapped using STAR and GENCODE V19 transcripts were quantified with RSEM using the standard ENCODE parameters.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files including gene expression estimates from RSEM and signal tracks in bigwig format
|
| |
|
| Submission date |
Apr 20, 2018 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Yin Shen |
| E-mail(s) |
Yin.Shen@ucsf.edu
|
| Phone |
4155023403
|
| Organization name |
UCSF
|
| Department |
Department of Neurology
|
| Lab |
Shen Lab
|
| Street address |
513 Parnassus Ave
|
| City |
SAN FRANCISCO |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94143-0410 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE113482 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [RNA-Seq] |
| GSE113483 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes |
|
| Relations |
| BioSample |
SAMN08965071 |
| SRA |
SRX3981937 |
